Installing RUMP/Genplot in Linux! (finally)

Posted in Linux, School, Science! by Cameron Kopas | No Comments »
My research requires that I use Rutherford Backscattering Spectroscopy to analyze samples at least a few times a week.  I use this amazing technique to characterize multilayer samples, and regularly get information such as: composition by layer, contaminants present, layer thickness/structure, and crystallinity.  There is a powerful (albeit command line) software package available for analyzing these files, called RUMP/Genplot, but it has so far been only available for Windows. (well it was “available” for Linux, DOS, and OS/2, but the professor who wrote it never responded to my emails requesting a Linux copy).
Anyway, I was very pleased to learn recently that the program has gone from a paid license, to being completely free.  Even more recently, they posted the source filename (previously completely hidden) with a note that an experienced user should be able to find the file.   This meant that I could perform data analysis on my own computer, and not have to run down to the iBeam lab every time i wanted to re-check some results!
Well, needless to say, I finally managed to get RUMP/Genplot for RBS analysis compiled on Linux, I suspect it will work the same way on OSX, Solaris, or any of the exotic UNIX variants that the program is compatible with.

first, download the source code tarball at:

(the filename might have to be updated with future versions)

if the user is on a mac, they need to install Xcode first (free, form the apple app store ).  any *NIX distribution should already have a c compiler installed.

due to the nature of the makefiles, you have to copy it to the “home” user directory, not any downloads directory, so in the terminal, cd to the downloads directory, then;  (note, the $ preceding each line indicates that this line is to be entered into the terminal, it is not a command itself)

$  mv ./cgs32j.tar.gz ~/cgs32j.tar.gz
move to the main user directory
$  cd ~/
then unzip

$ tar -xzf cgs32j.tar.gz

then move into the new directory
$  cd ./cgs

now you need to choose the correct makefile for your operating system.

$  ls

will output a list of the files in the directory.  makelnx is “Makefile for Linux”  and makeosx is “makefile for OSX”

choosing the makefile for your system,  run it using make -f.  the -f flag allows you to choose a particular file, otherwise “make” will be confused by the multiple files available

$  make -f makelnx

wait for that to finish, then as long as it ends with “leaving directory[…]”  and does not spit out any errors, its done.
The program is all command line, so it must be launched from the terminal each time,  to launch, open a terminal, cd to the ~/cgs/bin directory and start it using:
$  ./rump

then you can use the program as normal.

sweet!  maybe now i’ll write a “getting started with RUMP/GENPLOT” article, since learning basic analysis is horrible.

Vegan Gyro & Tzatziki Recipe.

Posted in Food, Guides, Life in General by Cameron Kopas | No Comments »

I want to preface this post by letting you know that my browser’s spellcheck wants to replace “tzatziki” with “Kazantzakis” as in the author of Zorba the Greek.

Since I have been experimenting with vegan(ism?) for awhile (okay fine, it was a dare), I have been really craving a few things; buffalo wings, and gyros. The worst thing is that people are always eating buffalo wings at the bars I go to, and people are always eating gyros at the Mediterranean places I eat. So I have the good fortune of being constantly exposed to what I really want to eat, but cannot.


Tzatziki Recipe

You’ll want to start the tzatziki first, because it needs to sit for at least an hour in the refrigerator.  This is adapted from a combination of a dozen or so tzatziki recipes that I found online.

  • 16 oz (2 cups)  soy yogurt (unflavored)
  • lemon juice (1 1/2 Tbsp) (or 1/2 lemon)
  • 3 tsp minced garlic
  • salt & pepper to taste (15 grinds salt, 6 grinds pepper)
  • Dill weed (1/4 cup fresh, or 4 tsp dried)
  • olive oil (2 tsp)

I’m not sure if the olive oil is strictly necessary, but I added it anyway. I have also heard a suggestion to replace salt with celery salt, which is much stronger, but would probably taste pretty good.

Mix these ingredients well, I used an immersion blender for this. After blending, add the cucumber and again mix well.

  • cucumber (~1 1/3 cup,  finely diced, deseeded)

Once again, I’m uncertain whether deseeding is really necessary, and I only deseeded half of  my cucumber. This came from one fairly long cucumber, but I assume two normal sized cucumbers would work just as well.

If you don’t know how to dice a cucumber, you cut it in half lengthwise (at this point you can de-seed with a spoon), then cut it into long thin strips, line all the strips up, and go to town without chopping off your fingertips.

Thats all! refrigerate at least one hour to let the flavors mix.


Gyro Meat

Now Gyro is typically a mixture of lamb, beef, and spices (you get three guesses to figure out how many of those are vegan!). So, I replaced the meat with yves Meatless ground ( veg/vegan/kosher:parve ground beef replacement containing wheat & soy), and combined some spice recipes for meat gyro. This stuff smells horrible when you open the package, but actually tastes pretty good.

  • 1 package Yves Meatless Ground (12oz approxeq 1lb “meat”)
  • 1 1/2 tsp Dried Oregano
  • 1 tsp Garlic Powder
  • 1 tsp Onion Powder
  • 1 tsp Salt
  • 3/4 tsp Pepper

Mix all that stuff together in a bowl, and prepare to get really frustrated. The yves has a weird consistency since it has soybeans in it, but gyro meat is mashed really finely. What you’ll want to do is put the mixture  on the counter, cover it with wax paper, and smash it for about ten minutes. I ended up taking a rolling pin and rolling the whole thing really flat, then banging on it with the pin to try to crush it.

After the consistency is better, but still nowhere near where it needs to be, mould the whole thing into a really thin, flat layer (or a few), and cook on the stove on medium heat for about 5 minutes per side.  I at first tried making it into a log, cooking, and slicing (as you would with regular gyro meat), but this does not stick together well enough, so cooking it in patties the size you want to eat works well and sticks it together.  (If anybody has an idea for something to ass that would stick it otherwise, please let me know. I would say 1 egg, but thats not vegan…)


Put one of the “meat” patties on a pita bread with diced tomatoes, red onion, lettuce, and scoop some tzatziki on it! I know I’ve already said this, but it was the best food I’ve had since the last time I ate buffalo wings.

dangerously hipster?

Posted in Life in General by Cameron Kopas | No Comments »

Worried about becoming a hipster, I feel the only way to save myself (and the future!) is to record a list of some of the things I did today (the list may not be in chronological order). Hopefully future generations will find this log and find some cure to this horrible ailment.

This began the first day of my project cataloging photographically the places where the homeless sleep at night.  Most of the places I have noticed, or people have pointed out to me over the past few years have been fairly consistent, and they have some similarities.  At best, the project might help some of these people, and at the very least the project will be an interesting way to document a very real part of Tempe that many people would rather just ignore.

I went to the local indie coffeebar (Cartel Coffee Lab) no fewer than two times today, once to read for a little while before work, and the second time to hang out with chase and discuss potential art exhibits, which segues well into the next item–

Discussed and came with a ridiculous number of theoretical potential art projects, concept albums, performance art pieces, and exhibitions.

While at work, I performed RBS simulation on materials so obscure you probably haven’t heard of them (I couldn’t even figure out what some of the layer structures were…)

Went to Zia records twice, once to look for some particular records, and, not finding any, returning later to browse the 7″ vinyl with Chase to see if there is anything I might want that I hadn’t planned on. I ended up with a 45 of The Kinks (containing Rats and Apeman),  a British Sea Power 45 with “Please Stand Up” and “Gale Warnings in Viking North”,  and a CD of The Reverend Peyton’s Big Damn Band recording of “Peyton on Patton”, which is a tribute to the influential Delta Blues musician, Charley Patton.

After the coffeebar and the record shop, we went to the Tempe Farmers Market, and I picked up a few local organic Pink Lady apples (the best kind), and a lactose-free cheese (!?) that I had never heard of, and the guy running the store could not describe it as anything other than “you know, its very cheesey… like, it tastes a lot like cheese” (this description only furthered my interest).  The cheese in question is a Vlaskaas from “Beemster”, which is apparently a relatively new kind of dutch cheese, very soft, and tastes both sweet and sharp at the same time.

Additional photographs may include one of a train stopped for seemingly no reason, the inside of a (mostly) empty warehouse (housing only a table and chairs, and a boat), and a short 90 second video of a train and subsequently a light rail train passing by in opposite directions.


a poem composed by my phone’s autosuggest function, and, by proxy, myself.

Posted in Life in General, Quixotic, Stupidity by Cameron Kopas | No Comments »

“, I the a im that’s they never your think it strategy talking that gets its cool you if couches smoothing once don’t open recording droid HeIXE them possibly putting. ”

this piece demanded absolutely no effort on my part, and was only peripherally written by myself.  It is licensed under the newest creative commons license out there which allows you to do whatever the heck you want with it. thank you.

Tempe Town Lake rough panorama

Posted in Life in General, Pictures by Cameron Kopas | No Comments »

I saw on the news that the Tempe Town Lake’s dam had broken, but I didn’t realise that meant it was empty until I rode the light rail to work and saw it.  Once I started my tests at work, I ran back over to the lake and took some pictures.  It turns out you can climb down into the lake pretty easily now, so once I get my other camera’s battery charged, I should have some amazing pictures.

Here is a rough draft panorama I took this morning with the canon PowerShot A590 and CHDK.


This picture is resized to 50%, and it was cropped.  There are empty areas where I didn’t take pictures by mistake, but I was in a hurry.  I could also work on the projection a little, I think it should be flat in the middle and curved more on the edges.  I think I will climb further down for the next one as well.

Morning Science

Posted in Life in General, Science! by Cameron Kopas | No Comments »

two  pictures are below, one of a clear shirt, and another of the same shirt as viewed in a foggy bathroom mirror.

Now, putting on this shirt in the morning, I was very excited to see that there was no purple visible in the mirror’s fogged-up reflection, but the blue lines are fine (this was even more exaggerated a minute or so before I took the picture, look toward the top of the image for the most severe effect).

Even if you know it is there, and wanted to, you can’t really see any purple stripes in the fog.  I think the problem is almost the same as astronomers had seeing into forming stars- dust (or in our case, condensed water vapor) blocks light. The reason for this would be that shorter wavelengths are more easily blocked than longer ones (purple being of shorter wavelength than blue which is shorter than green; yellow; orange; red; and so on).

Astronomers solved this problem by instead of looking at the visible wavelengths, building telescopes which record (higher wavelength) Infrared light data.  They could then see through those bothersome clouds of dust surrounding all of the cool stuff going on at the birth of a star.

Unfortunately, I don’t have infrared-vision yet, so for now I’ll have to settle for just not looking for purple in a foggy mirror.


Posted in Life in General, Science! by Cameron Kopas | No Comments »

Moved into my apartment yesterday morning, and of course, I forgot plenty of things.  One of these happened to be a shower curtain.

duct tape and plastic bags

Well while it doesn’t look very effective, the duct-tape and space bags worked great.  No water escaped the tub.  I’m still going to get a real shower curtain though, and as soon as possible.

Weekend Tailoring

Posted in Life in General by Cameron Kopas | No Comments »

Two weekends ago included a small family reunion (my grandfather’s 80th birthday party), which involved 20 people staying in my house (surprisingly, not uncomfortable at all), an interesting time at the new(er) arrowhead Melting Pot, and one of my brothers and I finally tailoring a few of our shirts.

The first thing I did was remove the collar from two shirts.  These were completely worn out, and since I still do laundry at home (moving into my apartment, with laundry, in 3 days!) my mother throws out/donates anything she sees that is  damaged.

thus is the penance for wearing stiff collars. closeup!

So, with my admiration for the Mandarin Collar (although I’ve probably only ever seen a handful), and with motivation from a recent post on Free-Man, the offending fabric was ripped out, and the seam was stitched back shut.

still has some pinholes and threads, needs to be washed.

The collar was removed on three shirts.

I then finally went and took in two shirts, my first being the purple checked shirt that I posted earlier. ( I have no good photos of the results. )

One shirt which had the collar damaged also had worn out cuffs, and was also too large.  That one got converted to a shirt-sleeved shirt, collar removed, and fitted.

Since that weekend I have altered at least 5 shirts, and repaired one pair of jeans (replaced/repaired the back pocket, re-sewed the seam since it was coming apart.

Brain Crack

Posted in Life in General by aliencam | No Comments »

Well I tool the opportunity recently to watch ZeFrank’s Brain Crack video once again (reference to it came up in a Lifehacker article again, and that is a great article). I’m thinking about it seriously now instead of just laughing about how hilariously funny the video is, and I think this could be an effective life motto. Instead of blathering on some more, here is the transcript.

Hungry Hippo licks Aunt JEmima [sic] writes, “Are you ever gonna break into song again? Are you running out of ideas?” Hungry Hippo licks Aunt JEmima, that’s a good question. I run out of ideas every day! Each day I live in mortal fear that I’ve used up the last idea that’ll ever come to me. If you don’t wanna run out of ideas the best thing to do is not to execute them. You can tell yourself that you don’t have the time or resources to do ’em right. Then they stay around in your head like brain crack. No matter how bad things get, at least you have those good ideas that you’ll get to later.

Some people get addicted to that brain crack. And the longer they wait, the more they convince themselves of how perfectly that idea should be executed. And they imagine it on a beautiful platter with glitter and rose petals. And everyone’s clapping for them. But the, but the, but the, but the bummer is most ideas kinda suck when you do ’em. And no matter how much you plan you still have to do something for the first time. And you’re almost guaranteed the first time you do something it’ll blow. But somebody who does something bad three times still has three times the experience of that other person who’s still dreaming of all the applause. When I get an idea, even a bad one, I try to get it out into the world as fast as possible, ’cause I certainly don’t want to be addicted to brain crack.

and the embedded video.

soundtrack for this post:
Phoenix – North
Phoenix – Girlfriend (wow two Phoenix songs in a row on shuffle, cool.)
The Cab – Zzzzz


Middle Mouse Scrolling in Ubuntu 10.04 Lucid Lynx

Posted in Guides, Linux, Ubuntu by aliencam | No Comments »

For this release, Ubuntu switched away from hal/udev  and went back to the old xorg configuration (I like this much better). There have been improvements and changes to the xorg.conf since we last used it (8.10 wow that’s been a long time!)  so now instead of putting everything in one giant /etc/X11/xorg.conf file and risking a single typo from breaking your x-server, we can put files in xorg.conf.d . This splits up configuration files so they can be more easily organised.

Here are the steps to get the middle-mouse scrolling again in Ubuntu 10.04, the Lucid Lynx. This should work for just about every thinkpad, and this same procedure will work in any Linux operating system using the xorg.conf.d method (if the /usr/lib/X11/xorg.conf.d/ folder doesn’t exist, then your distro is probably not using this method).

Begin by opening a terminal, and editing/creating the configuration file:
sudo gedit /usr/lib/X11/xorg.conf.d/20-thinkpad.conf

Now, paste in the following contents:
Section "InputClass"
Identifier "Trackpoint Wheel Emulation"
MatchProduct "TPPS/2 IBM TrackPoint|DualPoint Stick|Synaptics Inc. Composite TouchPad / TrackPoint|ThinkPad USB Keyboard with TrackPoint"
MatchDevicePath "/dev/input/event*"
Option "EmulateWheel" "true"
Option "EmulateWheelButton" "2"
Option "Emulate3Buttons" "false"
Option "XAxisMapping" "6 7"
Option "YAxisMapping" "4 5"
Option "EmulateWheelTimeout" "200"

you’ll probably want to delete and re-type all of those quotation marks, I don’t trust wordpress’ “code” tags to keep those straight. Then you’re ready to save and close the file. A quick restart of X (reboot your computer, or ctrl-alt-backspace if you enabled that in System > Preferences > Keyboard > Layouts > Options > Key Sequence to Kill the X Server > check the box. )

The line “EmulateWheelTimeout” is not absolutely necessary, but it does help prevent things from being randomly pasted everywhere whenever you try to scroll (for some reason people think it is funny to automatically map middlemouse to “paste”).

Sources: (yes, I just cited myself.)


Creative Commons License